A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the fmalmeida/mpgap analysis pipeline. For information about how to interpret these results, please see the documentation.
Report
generated on 2024-03-06, 01:19 -03
based on data in:
/array1/falmeida/NF_WORK/9c/ec4d4577a92fe1fac96da940917e82
General Statistics
| Sample Name | N50 (Kbp) | Assembly Length (Mbp) |
|---|---|---|
| canu_assembly | 3713.7Kbp | 29.8Mbp |
| canu_medaka_consensus | 3718.5Kbp | 29.9Mbp |
| flye_assembly | 2284.2Kbp | 29.3Mbp |
| flye_medaka_consensus | 2285.3Kbp | 29.3Mbp |
| raven_assembly | 3783.5Kbp | 29.5Mbp |
| raven_medaka_consensus | 3782.3Kbp | 29.5Mbp |
| shasta_assembly | 136.8Kbp | 28.3Mbp |
| shasta_medaka_consensus | 136.4Kbp | 28.3Mbp |
| wtdbg2_assembly | 2043.8Kbp | 28.6Mbp |
| wtdbg2_medaka_consensus | 2047.7Kbp | 28.6Mbp |
QUAST
QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.
Assembly Statistics
| Sample Name | N50 (Kbp) | L50 (K) | Largest contig (Kbp) | Length (Mbp) |
|---|---|---|---|---|
| canu_assembly | 3713.7Kbp | 0.0K | 4875.4Kbp | 29.8Mbp |
| canu_medaka_consensus | 3718.5Kbp | 0.0K | 4881.8Kbp | 29.9Mbp |
| flye_assembly | 2284.2Kbp | 0.0K | 3007.5Kbp | 29.3Mbp |
| flye_medaka_consensus | 2285.3Kbp | 0.0K | 3009.4Kbp | 29.3Mbp |
| raven_assembly | 3783.5Kbp | 0.0K | 4871.8Kbp | 29.5Mbp |
| raven_medaka_consensus | 3782.3Kbp | 0.0K | 4874.1Kbp | 29.5Mbp |
| shasta_assembly | 136.8Kbp | 0.1K | 479.0Kbp | 28.3Mbp |
| shasta_medaka_consensus | 136.4Kbp | 0.1K | 478.2Kbp | 28.3Mbp |
| wtdbg2_assembly | 2043.8Kbp | 0.0K | 3931.6Kbp | 28.6Mbp |
| wtdbg2_medaka_consensus | 2047.7Kbp | 0.0K | 3937.9Kbp | 28.6Mbp |
Number of Contigs
This plot shows the number of contigs found for each assembly, broken down by length.
BUSCO
BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.DOI: 10.1093/bioinformatics/btv351.
Lineage: fungi_odb10
fmalmeida/mpgap Software Versions
are collected at run time from the software output.
| Process Name | Software | Version |
|---|---|---|
| CUSTOM_DUMPSOFTWAREVERSIONS | python | 3.9.16 |
| yaml | 5.4.1 | |
| Workflow | Nextflow | 23.10.0 |
| fmalmeida/mpgap | 3.2 | |
| canu | canu | 2.2 |
| flye | flye | 2.9.2-b1786 |
| medaka | medaka | 1.11.1 |
| quast | busco | 5.6.1 |
| quast | v5.2.0 | |
| raven | raven | 1.6.1 |
| shasta | shasta | 0.11.1 |
| wtdbg2 | wtdbg2 | 2.5 |